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        <h1>Glossary</h1>
		<p><b><a name="Absolute_Quantification">Absolute Quantification</a>:</b> 
		determination of the number of target molecules, based on an absolute 
		quantitative scale generated by a quantitative standard. Using 
		conventional qPCR methods, this requires construction of a 
		target-specific standard curve, as compared to LRE in which absolute 
		scale is determined by <a href="#OCF">optical calibration</a> using 
		lambda gDNA as a universal quantitative standard. </p>
		<p><b><a name="Amplicon_Database">Amplicon Database</a>:</b> is a 
		database file with a *.amp extension that stores amplicon information</p>
		<p><b><a name="Amplification_profile">Amplification profile</a>:</b> is 
		the fundamental unit of real-time PCR in which the increase in amplicon 
		DNA is determined by measuring reaction fluorescence at the end of each 
		cycle. Also referred to as the <a href="#FC_Plot">F<sub>C</sub> plot</a>, 
		an amplification profile is generated by plotting reaction fluorescence 
		against cycle number.&nbsp; </p>
		<p><b><a name="Average_F0">Average F<sub>0</sub></a>:</b> target 
		quantity expressed in fluorescence units, produced by averaging the
		<a href="#Cycle_F0">cycle F<sub>0</sub></a> values generated by the 
		cycles within the <a href="#LRE_Window">LRE window</a>.</p>
		<p><a name="Average_Profile"><b>Average Profile</b>:</a> an 
		amplification profile generated by averaging, for each cycle, the 
		fluorescence readings from the 
		corresponding <a href="#Replicate_Profile">replicate profiles</a> to 
		produce a &quot;average&quot; amplification profile. 
		Average profiles are automatically constructed by the LRE Analyzer 
		during data import. Although this can greatly increase the <a href="#Read_Precision">read precision</a> that in 
		turn increases the precision of target quantification, it does assume 
		that the respective replicate profiles are sufficiently clustered. </p>
		<p>This becomes an issue with target quantities that are below 10 
		molecules per reaction, due to the impact of Poisson Distribution. Under 
		such situations, target quantity must be determined by averaging the 
		quantities produced by each individual replicate reaction. A detailed 
		description of the impact of Poisson Distribution is presented in the
		<a href="../quantitative_accuracy/less_than_10molecules.html">&lt;10 Target 
		Molecule Problem</a> section.</p>
		<p><b><a name="Average_Replicate_F0_CV">Average Replicate-F<sub>0</sub> 
		CV</a>: </b>is an indicator of the overall precision of target 
		quantification, based on the variation (CV) of&nbsp; F<sub>0</sub> 
		determinations generated by the technical replicates contained within 
		either an Experiment or Calibration database</p>
		<p><b><a name="C1/2">C<sub>1/2</sub></a></b>: the fractional cycle at 
		which reaction fluorescence reaches half of <a href="#Fmax">F<sub>max</sub></a> 
		(which roughly corresponds to the middle of most amplification profiles) 
		and is primarily used to define the position of an amplification 
		profile, similar but not identical to that of C<sub>q</sub> (AKA C<sub>t</sub> 
		and C<sub>p</sub>).</p>
		<p><b><a name="Calibration_Profile">Calibration Profile</a></b>: an 
		amplification profile generated by amplification of a known quantity of 
		lambda genomic DNA, from which an <a href="#OCF">
		optical calibration factor</a> is generated.</p>
		<p><b><a name="Calibration_Database">Calibration Database</a>:</b>&nbsp; 
		is a database file with a *.cal extension, containing
		<a href="#Calibration_Profile">calibration profiles</a> generated by the 
		same <a href="#Reaction_Setup">reaction setup</a></p>
		<p><b><a name="Cycle_Efficiency">Cycle Efficiency</a></b>: generally referred to as E<sub>C</sub>, defines amplification 
		efficiency as the increase in amplicon DNA quantity produced over a 
		single cycle, relative to the amount of amplicon DNA present at the 
		beginning of the cycle. For real-time PCR using SYBR Green I, the amount 
		of amplicon DNA present at the end of a cycle is reflected by the 
		fluorescence reading generated by that cycle (F<sub>C</sub>), whereas 
		the amount of amplicon DNA present at the beginning of the cycle is 
		reflected by the fluorescent reading produced by the previous cycle 
		(F<sub>C-1</sub>). Cycle efficiency, which is normally expressed as a 
		percentage, is calculated by dividing the these two values:</p>
		<p align="center">
		<map name="FPMap1">
		<area href="#Cycle_Efficiency" shape="rect" coords="1, 12, 30, 45">
		<area href="#Cycle_FC" shape="rect" coords="53, 0, 84, 29">
		</map>
		<img border="0" src="images/cycle_efficiency.gif" width="187" height="58" usemap="#FPMap1"></p>
		<p><b><a name="Cycle_FC">Cycle F<sub>C</sub></a>:</b> the reaction 
		fluorescence generated at the end of the cycle, which with SYBR Green I 
		detection is proportional to the amount of amplicon DNA. </p>
		<p><b><a name="Cycle_F0">Cycle F<sub>0</sub></a>:</b> is the target 
		quantity derived from the cycle&#39;s fluorescence reading (<a href="#Cycle_FC">F<sub>C</sub></a>), 
		calculated using a derivative of the classic Boltzmann sigmoid function:</p>
		<p align="center"><map name="FPMap2">
		<area href="#Fmax" shape="rect" coords="106, 0, 157, 23">
		<area href="#Fmax" shape="rect" coords="71, 23, 114, 49">
		<area href="#Cycle_FC" shape="rect" coords="69, 49, 113, 72">
		<area href="#Emax" shape="rect" coords="144, 33, 187, 63">
		<area href="#Cycle_F0" shape="rect" coords="0, 6, 27, 36">
		</map>
		<img border="0" src="images/Fo_equation.gif" width="230" height="73" usemap="#FPMap2"></p>
		<p>
		<span lang="EN-US" style="font-size: 11.0pt; font-family: Arial; font-weight:700">
		<a name="deltaE">ΔE</a></span><b>:</b> is the rate of loss in amplification 
		efficiency, determined from the slope of the <a href="#LRE_plot">LRE 
		plot</a>.</p>
		<p><b><a name="Emax">E<sub>max</sub></a></b>: the maximal amplification 
		efficiency, determined by the Y-intercept of the <a href="#LRE_plot">LRE plot</a> 
		and is equivalent to the amplification efficiency as defined by the 
		slope of a standard curve used in conventional qPCR.</p>
		<p><b><a name="Experiment_Database">Experiment Database</a>:</b> is a 
		database file with a *.exp extension, in which a group of related runs 
		are stored, along with their associated <a href="#Sample_Profile">sample 
		profiles</a></p>
		<p><b><a name="FC_Plot">F<sub>C</sub> Plot</a>:</b> a plot of the
		<a href="#Cycle_FC">cycle F<sub>C</sub></a> generated by an 
		amplification reaction vs. cycle number (generally referred to as the 
		&quot;amplification profile&quot; or profile for short) that in the LRE 
		analyzer also includes the 
		predicted cycle F<sub>C</sub> generated by the <a href="#LRE_Model">LRE 
		model</a>. </p>
		<p><b><a name="Fmax">F<sub>max</sub></a>:</b> the maximal reaction 
		fluorescence that defines the predicted top of an amplification profile, 
		which is also referred to as the plateau phase, and can be calculated 
		using this equation:</p>
		<p align="center"><map name="FPMap4">
		<area href="#Emax" shape="rect" coords="55, 3, 98, 28">
		<area href="#deltaE" shape="rect" coords="51, 31, 102, 50">
		</map>
		<img border="0" src="images/Fmax_equation.gif" width="103" height="51" usemap="#FPMap4"></p>
		<p><b><a name="F0_Threshold">F<sub>0</sub> Threshold</a>:</b> expressed 
		as the percent difference from the <a href="#Average_F0">average F<sub>0</sub></a>, 
		the F<sub>0</sub> threshold is used to determined if a cycle should be 
		included into the <a href="#LRE_Window">LRE window</a>, based on 
		comparing its <a href="#Cycle_F0">cycle F<sub>0</sub></a> to the
		<a href="#Average_F0">average F<sub>0</sub></a>. </p>
		<p><b><a name="High_Quality_Profiles">High Quality Profiles</a>:</b> are 
		profiles generated with good <a href="#Read_Precision">read precision</a> 
		and amplification kinetics that conforms well to the
		<a href="#LRE_Model">LRE model</a>. The performance of the primer pair 
		is another key parameter that impacts both the repeatability and 
		accuracy of target quantification. </p>
		<p><b><a name="LRE_Analysis">LRE Analysis</a>:</b> the process of 
		generating values for the two parameters the govern PCR amplification (<span lang="EN-US" style="font-size: 11.0pt; font-family: Arial"><a href="../glossary/glossary.html#deltaE">ΔE</a></span> 
		and <a href="#Emax">E<sub>max</sub></a>) by applying linear regression 
		analysis to the <a href="#LRE_plot">LRE Plot</a>. </p>
		<p><b><a name="LRE_Model">LRE Model</a>:</b> based on the assumption 
		that reaction fluorescence (F<sub>C</sub>) is proportional to amplicon 
		DNA mass, PCR amplification can be modeled using the equation:</p>
		<p align="center"><map name="FPMap3">
		<area href="#Cycle_FC" shape="rect" coords="2, 11, 30, 37">
		<area href="#Fmax" shape="rect" coords="122, 0, 162, 24">
		<area href="#Fmax" shape="rect" coords="77, 28, 118, 54">
		<area href="#Average_F0" shape="rect" coords="74, 53, 117, 80">
		<area href="#Emax" shape="rect" coords="153, 36, 196, 67">
		</map>
		<img border="0" src="images/LRE_model.gif" width="244" height="81" usemap="#FPMap3"></p>
		<p align="left">Derived by adapting the classic Boltzmann sigmoid to 
		PCR, this allows 
		the conformity of an amplification profile to be assessed, which among 
		other things, can reveal aberrant amplification kinetics. </p>
		<p><b><a name="LRE_plot">LRE Plot</a>:</b> a plot of cycle efficiency (<a href="#Cycle_Efficiency">E<sub>C</sub></a>) 
		vs. reaction fluorescence (<a href="#Cycle_FC">F<sub>C</sub></a>) that 
		generates a linear representation of an amplification profile:</p>
		<p align="center">
		<b>The LRE Plot</b><br>
		<img border="0" src="../editor_panel/images/lre_plot.gif" width="360" height="210"></p>
		<p>LRE originated from the ability to define the kinetics of amplification 
		by applying linear regression analysis to the LRE plot, using the equation: </p>
		<p align="center"><map name="FPMap0">
		<area href="#Cycle_FC" shape="rect" coords="0, 1, 32, 26">
		<area href="#deltaE" shape="rect" coords="47, 0, 84, 26">
		<area href="#Cycle_FC" shape="rect" coords="93, 0, 122, 26">
		<area href="#Emax" shape="rect" coords="137, 0, 181, 26">
		</map>
		<img border="0" src="images/LRE_linear_equation.gif" width="184" height="27" usemap="#FPMap0">&nbsp; </p>
		<p><b><a name="LRE_Window">LRE Window</a>:</b> consists of a contiguous 
		group of cycles within the central region of an amplification profile 
		that is used for <a href="#LRE_Analysis">LRE analysis</a>.</p>
		<p><b><a name="Minimum_FC_Setting">Minimum F<sub>C</sub> Setting</a>:</b> 
		used for automated <a href="#LRE_Window">LRE window</a> selection in 
		which the first cycle that generated a F<sub>C</sub> above the specified 
		minimum F<sub>C</sub> is designated as the <a href="#Start_Cycle">start 
		cycle</a>. If not specified the first cycle below <a href="#C1/2">C<sub>1/2</sub></a> 
		is designated at the start cycle.</p>
		<p><b><a name="MO">M</a><sub>0</sub></b>: the DNA mass of the amplicon 
		region within the target, expressed in nanograms of double stranded DNA. 
		As described in the
		<a href="../optical_calibration/optical_calibration_overview.html">
		optical calibration overview</a>, M<sub>0</sub> can be converted into 
		the number of target molecules based on the amplicon size. </p>
		<p><b><a name="Optical_Calibration">Optical Calibration</a>:</b> the 
		process of calibrating the fluorescence units generated from an assay by 
		amplifying a known quantity of lambda gDNA to produce a
		<a href="#Calibration_Profile">calibration profile</a>, from which an
		<a href="#OCF">optical calibration factor</a> is derived. </p>
		<p><b><a name="OCF">Optical Calibration Factor</a>:</b> or OCF, 
		correlates fluorescence units to amplicon DNA mass. As described in the
		<a href="../optical_calibration/optical_calibration_overview.html">
		optical calibration overview</a> an OCF&nbsp; is used to 
		convert target quantities from fluorescence units to the number of 
		target molecules.</p>
		<p><b><a name="Reaction_Setup">Reaction Setup</a>:</b> encompasses all 
		of the factors impacting the optics of an assay, such as the reaction 
		vessel and closure, the enzyme formulation and the optics of the 
		instrument. As a whole these parameters determine the fluorescence 
		intensity of an assay. A key aspect of implementing absolute 
		quantification is <a href="#Optical_Calibration">optical calibration</a> 
		in which the fluorescence intensity of an assay is quantified, 
		generating an <a href="#OCF">optical calibration factor</a> that defines 
		the reaction setup used to conduct an assay.</p>
		<p><b><a name="Read_Precision">Read Precision</a>:</b> the precision of 
		the fluorescence readings taken the end of each cycle, which is 
		dependent in large part on the optical system of the instrument. Read 
		precision can play a major role in the efficacy of
		<a href="#LRE_Analysis">LRE analysis</a>. </p>
		<p><b><a name="Replicate_Profile">Replicate Profiles</a></b>: profile 
		generated by technical 
		replicate reactions. To increase optical precision, replicate profiles are used to generate an
		<a href="#Average_Profile">average profile</a>.</p>
		<p><b><a name="Sample_Profile">Sample Profile</a></b>: an amplification 
		profile generated from a sample (AKA an unknown).</p>
		<p><b><a name="Start_Cycle">Start Cycle</a></b>: the first cycle within 
		the bottom of the <a href="#LRE_Window">LRE window</a>. </p>
		<p>&nbsp;</p>
		<p>&nbsp;</p>
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